Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. A report describing the software has been published; see He, J., Dai, X. and Zhao, X. (2007). PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioninformatics 8:53.

MET-IDEA 2.04 has the following new features compared with previous release 2.02: (1) Microsoft .net 1.1 has been replaced with .net version 2; (2) manual curation of peak integration;(3) display of mass spectrum. MET-IDEA is freely available to academic users upon request. A manuscript describing new features is under preparation.

The MET-IDEA 2.0 has the following new features compared with its previous versions: (1) more accurate for high resolution data such as those generated by LC devices; (2) graphic presentation available for detected peaks; (3) more efficient in memory usage. MET-IDEA is freely available to academic users upon request.

A current and significant limitation to metabolomics is the large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into organized data matrices necessary for further statistical processing and data visualization. This article describes a new data extraction tool, MET-IDEA (Metabolomics Ion-Based Data Extraction Algorithm) which surmounts this void. MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semi-quantitative data from raw data files, which allows for more rapid biological insight. MET-IDEA is freely available to academic users upon request. A report describing the software has been published; see Broeckling CD, Reddy IR, Duran AL,Zhao X and Sumner LW. MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal Chem. 2006 Jul 1;78(13):4334-41.